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Bioinformatics Advance Access originally published online on December 21, 2004
Bioinformatics 2005 21(8):1572-1578; doi:10.1093/bioinformatics/bti238
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Quick and simple: quality control of microarray data

Ursula Sauer *, Claudia Preininger and Robert Hany-Schmatzberger

ARC Seibersdorf research GmbH, Department Bio-resources A-2444 Seibersdorf, Austria

*To whom correspondence should be addressed.

Motivation: Microarrays are high-throughput tools for parallel miniaturized detection of biomolecules. In contrast to experiments using ratios of signals in two channels, experiments with only one fluorescent dye cause special problems for data analysis. The present work compares algorithms for quality filtering on spot level as well as array/slide level.

Results: Methods for quantitative spot filtering are discussed and new sets of quality scores for data preprocessing are designed. As measures of spot quality also reflect the quality of protocols, they were employed to find the optimal print buffer in an optimization experiment. In order to determine problematic arrays within a set of replicates we tested methods of outlier detection which can suitably replace the visual inspection of slides.

Contact: Ursula.Sauer{at}arcs.ac.at


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